Plant Circular RNA Database

Detail information of GLYMA_15G046000_circ_g.2

			
						 General Information
					
						CircRNA Name
						GLYMA_15G046000_circ_g.2
					
						ID in PlantcircBase
						gma_circ_003996
					
						Alias
						Gm15circRNA404, gma-circRNA2126
					
						Organism
						
							Glycine max						
					
						Position
						
							chr15: 3669200-3670897  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI, find_circ
					
						Parent gene
						
							GLYMA_15G046000						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_15G046000_circ_g.1 GLYMA_15G046000_circ_g.3 GLYMA_15G046000_circ_g.4 GLYMA_15G046000_circ_g.5 						
					
						Support reads
						NA
					
						Tissues
						leaf, root, stem, flower bud
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						KRH10416:7
KRH10417:7

General Information
CircRNA Name	GLYMA_15G046000_circ_g.2
ID in PlantcircBase	gma_circ_003996
Alias	Gm15circRNA404, gma-circRNA2126
Organism	Glycine max
Position	chr15: 3669200-3670897 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI, find_circ
Parent gene	GLYMA_15G046000
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_15G046000_circ_g.1 GLYMA_15G046000_circ_g.3 GLYMA_15G046000_circ_g.4 GLYMA_15G046000_circ_g.5
Support reads	NA
Tissues	leaf, root, stem, flower bud
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	KRH10416:7 KRH10417:7

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							TTTCCACTTACGTTTTAAAGAAATGATAGCCTGAAGTCTAACATCTTCATGAAAATAACTGGAG
TGTTTAACCAAGATTCTTAGTGTCTCGTCCAAGTAGttcaaagcttgttcatgaccatttttgc
acaactctcccacacaaaatgcagcattccttctattagttgcctcagatgatgctagttcttt
aagtacca

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 711
Transcript exons: 3669200-3669312,3669436-3669531,3669603-3669820,3669899-
3670021,3670117-3670147,3670298-3670338,3670809-3670897
TTCAAAGCTTGTTCATGACCATTTTTGCACAACTCTCCCACACAAAATGCAGCATTCCTTCTAT
TAGTTGCCTCAGATGATGCTAGTTCTTTAAGTACCAAGGGCATCACCCTATCAACATAGCTTGC
AATAGGAGAACCCATGTTCTGAGCAACTTCAGCTAGGCAGGCAACTACCATAGTCCTATCTTGA
GGAGGACGAGAAGATTTAGCAAATTTCATTAGAGGTTCAAATAGCTGAGCAAAAATGGGAGCAA
ATTGAGCACCCATGGACTTTGCAAATGCAGGGAGAAGATCTGAAACTGCATCCATAAGCACTTC
ATCATGTGCACTGTCAACATCATCAATTTCACTGTCTGACTCTATCTGCTGACAGGCAGATTGC
TCCCGAAGCAACAATGAAGTTGCATCAACAAGCTGGGACAAGTAAGGCTCAAGAGTTGCATAAC
CATAATCTCTAATGATGTCAGCCACACTAGTGCAAGCTTGAGCAACCACTTCCTTGTCATCATC
TTCAACCATAGTCTTGATGTAAATATTCATCACAGTATCGAGAAGTTCTTTTGCTTTAGCAGCC
CCTTCATTTTGACTTTGGAAGATTGCATTGGCCGCAGTTAAAGTATGTTTTAAAGAAATGATAG
CCTGAAGTCTAACATCTTCATGAAAATAACTGGAGTGTTTAACCAAGATTCTTAGTGTCTCGTC
CAAGTAG
						
					

						Genomic sequence
						
							TTCAAAGCTTGTTCATGACCATTTTTGCACAACTCTCCCACACAAAATGCAGCATTCCTTCTAT
TAGTTGCCTCAGATGATGCTAGTTCTTTAAGTACCAAGGGCATCACCCTCTGAGAAAGATAATA
TCACATATTACAAATCAATTACAATTGTCAAAATTCCGACTTTAATTGAAAAATGGAATCACAA
AAGGAAAAAGTAAGAGAGATTAAGAAAAAGAGTAACAAAATTACATCAACATAGCTTGCAATAG
GAGAACCCATGTTCTGAGCAACTTCAGCTAGGCAGGCAACTACCATAGTCCTATCTTGAGGAGG
ACGAGAAGATTTCTGCATTTCAAAATGAGGATATTAATTTGTGATTTATTCCTAACAGTAAAAG
TTATTGGTTGCGAACTCACAGCAAATTTCATTAGAGGTTCAAATAGCTGAGCAAAAATGGGAGC
AAATTGAGCACCCATGGACTTTGCAAATGCAGGGAGAAGATCTGAAACTGCATCCATAAGCACT
TCATCATGTGCACTGTCAACATCATCAATTTCACTGTCTGACTCTATCTGCTGACAGGCAGATT
GCTCCCGAAGCAACAATGAAGTTGCATCAACAAGCTGGGACAAGTCTGATAGTAGAGTAAATCT
CACATTAGCATCAGCTCAGCAAAATGACTTTAAATGATAGATCAAAATTGTATGCTTACAAGGC
TCAAGAGTTGCATAACCATAATCTCTAATGATGTCAGCCACACTAGTGCAAGCTTGAGCAACCA
CTTCCTTGTCATCATCTTCAACCATAGTCTTGATGTAAATATTCATCACAGTATCTGATGAATC
AAACAGCCCCAAAAGGTTATACAGATAAAATGAAATGGCTTATCATTACCATAAAAAAATAAAA
TCAAACAGTAGATGTTCTCACCGAGAAGTTCTTTTGCTTTAGCAGCCCCTTCCTTAAAAACAAA
GGCAGTGTCAATTGTGGTGTTAAAATCAAACAAAAGATGGGAATGGGACCAAGAAACAAAATGA
TTAAATAAAAATAAGTCCTTCTATGATAAAGTAAGAATGCAAAGTTAAAACAAGGAGGTATTGG
TCAAACTTACATTTTGACTTTGGAAGATTGCATTGGCCGCAGTTAAAGTATCTGCGGTTAAAAT
CAAAAACACATCAGCAATCAATGGCAATACACACACACATAATCTATGGAGAAAAAAAACTTCC
GTATTTATTTGAGAACTCAAATAAGGTAGAAGGACATGTATACAAATTTGCAGGACAAAACATG
TACAATATCATACTCAGACAATAAAGACAGTTTACTTCCACTGAATTATATTTTTCCATCTTTT
CCTCATTGCTTTTGTATGAATATATGGTTTGATTGATAGGTTCATATATCATCATGGAACTCTA
TGGTATGTTATTCAGCATCATTCAGATTAATATTCTACATGGTACAATTCATTTTGCACTGAAA
CAACCAGAAACAATTATTTAAAAAAAGTACAAGGTTCCTGCCATGCATAAATGAGAGAAACTGC
AGAAAATGAGAATAGGTAAAACAAACAAGCATAATTTTAAAAACAGAACATTCTGAAAATAGTT
TCCACTTACGTTTTAAAGAAATGATAGCCTGAAGTCTAACATCTTCATGAAAATAACTGGAGTG
TTTAACCAAGATTCTTAGTGTCTCGTCCAAGTAG
						
					

			
		

Sequences
Splice junction sequence	TTTCCACTTACGTTTTAAAGAAATGATAGCCTGAAGTCTAACATCTTCATGAAAATAACTGGAG TGTTTAACCAAGATTCTTAGTGTCTCGTCCAAGTAGttcaaagcttgttcatgaccatttttgc acaactctcccacacaaaatgcagcattccttctattagttgcctcagatgatgctagttcttt aagtacca
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 711 Transcript exons: 3669200-3669312,3669436-3669531,3669603-3669820,3669899- 3670021,3670117-3670147,3670298-3670338,3670809-3670897 TTCAAAGCTTGTTCATGACCATTTTTGCACAACTCTCCCACACAAAATGCAGCATTCCTTCTAT TAGTTGCCTCAGATGATGCTAGTTCTTTAAGTACCAAGGGCATCACCCTATCAACATAGCTTGC AATAGGAGAACCCATGTTCTGAGCAACTTCAGCTAGGCAGGCAACTACCATAGTCCTATCTTGA GGAGGACGAGAAGATTTAGCAAATTTCATTAGAGGTTCAAATAGCTGAGCAAAAATGGGAGCAA ATTGAGCACCCATGGACTTTGCAAATGCAGGGAGAAGATCTGAAACTGCATCCATAAGCACTTC ATCATGTGCACTGTCAACATCATCAATTTCACTGTCTGACTCTATCTGCTGACAGGCAGATTGC TCCCGAAGCAACAATGAAGTTGCATCAACAAGCTGGGACAAGTAAGGCTCAAGAGTTGCATAAC CATAATCTCTAATGATGTCAGCCACACTAGTGCAAGCTTGAGCAACCACTTCCTTGTCATCATC TTCAACCATAGTCTTGATGTAAATATTCATCACAGTATCGAGAAGTTCTTTTGCTTTAGCAGCC CCTTCATTTTGACTTTGGAAGATTGCATTGGCCGCAGTTAAAGTATGTTTTAAAGAAATGATAG CCTGAAGTCTAACATCTTCATGAAAATAACTGGAGTGTTTAACCAAGATTCTTAGTGTCTCGTC CAAGTAG
Genomic sequence	TTCAAAGCTTGTTCATGACCATTTTTGCACAACTCTCCCACACAAAATGCAGCATTCCTTCTAT TAGTTGCCTCAGATGATGCTAGTTCTTTAAGTACCAAGGGCATCACCCTCTGAGAAAGATAATA TCACATATTACAAATCAATTACAATTGTCAAAATTCCGACTTTAATTGAAAAATGGAATCACAA AAGGAAAAAGTAAGAGAGATTAAGAAAAAGAGTAACAAAATTACATCAACATAGCTTGCAATAG GAGAACCCATGTTCTGAGCAACTTCAGCTAGGCAGGCAACTACCATAGTCCTATCTTGAGGAGG ACGAGAAGATTTCTGCATTTCAAAATGAGGATATTAATTTGTGATTTATTCCTAACAGTAAAAG TTATTGGTTGCGAACTCACAGCAAATTTCATTAGAGGTTCAAATAGCTGAGCAAAAATGGGAGC AAATTGAGCACCCATGGACTTTGCAAATGCAGGGAGAAGATCTGAAACTGCATCCATAAGCACT TCATCATGTGCACTGTCAACATCATCAATTTCACTGTCTGACTCTATCTGCTGACAGGCAGATT GCTCCCGAAGCAACAATGAAGTTGCATCAACAAGCTGGGACAAGTCTGATAGTAGAGTAAATCT CACATTAGCATCAGCTCAGCAAAATGACTTTAAATGATAGATCAAAATTGTATGCTTACAAGGC TCAAGAGTTGCATAACCATAATCTCTAATGATGTCAGCCACACTAGTGCAAGCTTGAGCAACCA CTTCCTTGTCATCATCTTCAACCATAGTCTTGATGTAAATATTCATCACAGTATCTGATGAATC AAACAGCCCCAAAAGGTTATACAGATAAAATGAAATGGCTTATCATTACCATAAAAAAATAAAA TCAAACAGTAGATGTTCTCACCGAGAAGTTCTTTTGCTTTAGCAGCCCCTTCCTTAAAAACAAA GGCAGTGTCAATTGTGGTGTTAAAATCAAACAAAAGATGGGAATGGGACCAAGAAACAAAATGA TTAAATAAAAATAAGTCCTTCTATGATAAAGTAAGAATGCAAAGTTAAAACAAGGAGGTATTGG TCAAACTTACATTTTGACTTTGGAAGATTGCATTGGCCGCAGTTAAAGTATCTGCGGTTAAAAT CAAAAACACATCAGCAATCAATGGCAATACACACACACATAATCTATGGAGAAAAAAAACTTCC GTATTTATTTGAGAACTCAAATAAGGTAGAAGGACATGTATACAAATTTGCAGGACAAAACATG TACAATATCATACTCAGACAATAAAGACAGTTTACTTCCACTGAATTATATTTTTCCATCTTTT CCTCATTGCTTTTGTATGAATATATGGTTTGATTGATAGGTTCATATATCATCATGGAACTCTA TGGTATGTTATTCAGCATCATTCAGATTAATATTCTACATGGTACAATTCATTTTGCACTGAAA CAACCAGAAACAATTATTTAAAAAAAGTACAAGGTTCCTGCCATGCATAAATGAGAGAAACTGC AGAAAATGAGAATAGGTAAAACAAACAAGCATAATTTTAAAAACAGAACATTCTGAAAATAGTT TCCACTTACGTTTTAAAGAAATGATAGCCTGAAGTCTAACATCTTCATGAAAATAACTGGAGTG TTTAACCAAGATTCTTAGTGTCTCGTCCAAGTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							csa_circ_001696 						
					
						PMCS
						0.443390307

Conservation Information
Conserved circRNAs	csa_circ_001696
PMCS	0.443390307

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3670015-3669202(-)
						
						Potential amino acid sequence
						
							MNIYIKTMVEDDDKEVVAQACTSVADIIRDYGYATLEPYLSQLVDATSLLLREQSACQQIESDS
EIDDVDSAHDEVLMDAVSDLLPAFAKSMGAQFAPIFAQLFEPLMKFAKSSRPPQDRTMVVACLA
EVAQNMGSPIASYVDRVMPLVLKELASSEATNRRNAAFCVGELCKNGHEQALNYLDETLRILVK
HSSYFHEDVRLQAIISLKHTLTAANAIFQSQNEGAAKAKELLDTVMNIYIKTMVEDDDKEVVAQ
ACTSVADIIRDYGYATLEPYLSQLVDATSLLLREQSACQQIESDSEIDDVDSAHDEVLMDAVSD
LLPAFAKSMGAQFAPIFAQLFEPLMKFAKSSRPPQDRTMVVACLAEVAQNMGSPIASYVDRVMP
LVLKELASSEATNRRNAAFCVGELCKNGHEQALNYLDETLRILVKHSSYFHEDVRLQAIISLKH
TLTAANAIFQSQNEGAAKAKELLDTVMNIYIKTMVEDDDKEVVAQACTSVADIIRDYGYATLEP
YLSQLVDATSLLLREQSACQQIESDSEIDDVDSAHDEVLMDAVSDLLPAFAKSMGAQFAPIFAQ
LFEPLMKFAKSSRPPQDRTMVVACLAEVAQNMGSPIASYVDRVMPLVLKELASSEATNRRNAAF
CVGELCKNGHEQALNYLDETLRILVKHSSYFHEDVRLQAIISLKHTLTAANAIFQSQNEGAAKA
KELLDTVMNIYIKTMVEDDDKEVVAQACTSVADIIRDYGYATLEPYLSQLVDATSLLLREQSAC
QQIESDSEIDDVDSAHDEVLMDAVSDLLPAFAKSMGAQFAPIFAQLFEPLMKFAKSSRPPQDRT
MVVACLAEVAQNMGSPIASYVDRVMPLVLKELASSEATNRRNAAFCVGELCKNGHEQAL(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3670015-3669202(-)
Potential amino acid sequence	MNIYIKTMVEDDDKEVVAQACTSVADIIRDYGYATLEPYLSQLVDATSLLLREQSACQQIESDS EIDDVDSAHDEVLMDAVSDLLPAFAKSMGAQFAPIFAQLFEPLMKFAKSSRPPQDRTMVVACLA EVAQNMGSPIASYVDRVMPLVLKELASSEATNRRNAAFCVGELCKNGHEQALNYLDETLRILVK HSSYFHEDVRLQAIISLKHTLTAANAIFQSQNEGAAKAKELLDTVMNIYIKTMVEDDDKEVVAQ ACTSVADIIRDYGYATLEPYLSQLVDATSLLLREQSACQQIESDSEIDDVDSAHDEVLMDAVSD LLPAFAKSMGAQFAPIFAQLFEPLMKFAKSSRPPQDRTMVVACLAEVAQNMGSPIASYVDRVMP LVLKELASSEATNRRNAAFCVGELCKNGHEQALNYLDETLRILVKHSSYFHEDVRLQAIISLKH TLTAANAIFQSQNEGAAKAKELLDTVMNIYIKTMVEDDDKEVVAQACTSVADIIRDYGYATLEP YLSQLVDATSLLLREQSACQQIESDSEIDDVDSAHDEVLMDAVSDLLPAFAKSMGAQFAPIFAQ LFEPLMKFAKSSRPPQDRTMVVACLAEVAQNMGSPIASYVDRVMPLVLKELASSEATNRRNAAF CVGELCKNGHEQALNYLDETLRILVKHSSYFHEDVRLQAIISLKHTLTAANAIFQSQNEGAAKA KELLDTVMNIYIKTMVEDDDKEVVAQACTSVADIIRDYGYATLEPYLSQLVDATSLLLREQSAC QQIESDSEIDDVDSAHDEVLMDAVSDLLPAFAKSMGAQFAPIFAQLFEPLMKFAKSSRPPQDRT MVVACLAEVAQNMGSPIASYVDRVMPLVLKELASSEATNRRNAAFCVGELCKNGHEQAL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a; Chen et al., 2018

circRNA

Detail information of GLYMA_15G046000_circ_g.2

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